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I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is category. According to MutSigCV, every mutation can be divided into the following categories:

  1. CpG transitions
  2. CpG transversions
  3. C: G transitions
  4. C: G transversions
  5. A: T transitions
  6. A: T transversions
  7. null+indel mutations

I am very much clear about some of this categories like C: G transversion and A: T transversion but for rest, I am unable to make any solid conceptual background. Can anyone suggest me the proper definition of these categories of mutations with proper examples?

Thanks.

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  • $\begingroup$ Did you try asking on the help forum? Or your problem is what is each mutation? $\endgroup$
    – llrs
    Jul 9 '18 at 11:39
  • $\begingroup$ @Llopis: Not yet. I even didn't know about that. I know only GATK forum and this website. I have googled these terms extensively but didn't get even proper definitions. That's why I started the bounty on this question. $\endgroup$ Jul 9 '18 at 12:35
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    $\begingroup$ CpG transversions are the same as C: G transversions, except that they are followed by a G which means they are potential targets for DNA methylation. Methylcytosine can undergo deamination to Thymine, which makes them mutation hotspots $\endgroup$ Jul 10 '18 at 14:43
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    $\begingroup$ indel = insertion/deletion. I have no idea what null means in this context $\endgroup$ Jul 10 '18 at 14:49
  • $\begingroup$ @heathobrien Those comments are an answer! With a link to a source you could get the bounty $\endgroup$
    – llrs
    Jul 11 '18 at 9:03

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